☰ Navigation Tabs
Crystal structure of a putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase from Oleispira antarctica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 20% PEG 4000, 10% 2-PROPANOL, 0.1M TRI-SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.02 α = 90 b = 76.02 β = 90 c = 241.121 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2009-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 50 98.6 0.063 27.29 4.91 44282 2 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 85.4 0.115 4.45 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1WBH 1.84 50 40941 2163 95.35 0.17957 0.17776 0.21433 0.1746 RANDOM 26.5
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.15 -1.08 -2.15 3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.557 r_dihedral_angle_3_deg 13.864 r_dihedral_angle_4_deg 13.343 r_dihedral_angle_1_deg 6.074 r_scangle_it 4.613 r_scbond_it 2.94 r_angle_refined_deg 1.694 r_mcangle_it 1.637 r_mcbond_it 0.952 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.557 r_dihedral_angle_3_deg 13.864 r_dihedral_angle_4_deg 13.343 r_dihedral_angle_1_deg 6.074 r_scangle_it 4.613 r_scbond_it 2.94 r_angle_refined_deg 1.694 r_mcangle_it 1.637 r_mcbond_it 0.952 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3196 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 12
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling